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View article: Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale Open
Proteomic and phenotypic cell sensitivity datasets are increasingly important for understanding chemoproteomics and the underlying drug mechanisms of action. Yet, integrating such heterogeneous datasets remains challenging due to inconsist…
View article: Systematic characterization of existing and novel inducible transgenic systems in human pluripotent stem cells after prolonged differentiation
Systematic characterization of existing and novel inducible transgenic systems in human pluripotent stem cells after prolonged differentiation Open
SUMMARY The ability to control transgene expression both temporally and quantitatively in human-relevant cells and tissues is a cornerstone of biomedical research. Additionally, precise transgene control is crucial for optimizing human cel…
View article: Comparison of Different Sites of Microbiota Shows Increased <i>Pseudomonas</i> Species in the Gut Mucosa in Inflammatory Bowel Disease
Comparison of Different Sites of Microbiota Shows Increased <i>Pseudomonas</i> Species in the Gut Mucosa in Inflammatory Bowel Disease Open
Background Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn’s disease (CD), is associated with changes in the gut microbiome. Studies comparing fecal, gut mucosal, and salivary microbiomes are rare, and questio…
View article: Reticulated platelets in coronary artery disease: a multidimensional approach unveils prothrombotic signalling and novel therapeutic targets
Reticulated platelets in coronary artery disease: a multidimensional approach unveils prothrombotic signalling and novel therapeutic targets Open
Background and Aims Reticulated platelets (RPs), hyperreactive and RNA-rich, are associated with increased risk of cardiovascular events and suboptimal response to antiplatelet therapy in coronary artery disease (CAD). However, the underly…
View article: Integrative gene and isoform co-expression networks reveal regulatory rewiring in stress-related psychiatric disorders
Integrative gene and isoform co-expression networks reveal regulatory rewiring in stress-related psychiatric disorders Open
Isoform-specific expression patterns have been linked to stress-related psychiatric disorders such as major depressive disorder (MDD). To further explore their involvement, we constructed co-expression networks using total gene expression …
View article: Drugst.One DREAM - Drug Repurposing through Expert Annotation and Modification
Drugst.One DREAM - Drug Repurposing through Expert Annotation and Modification Open
Complex diseases often lack an actionable understanding of their underlying causal biological mechanisms, which leads to treating symptoms rather than causes. Network and systems medicine define disease mechanisms through disease-associate…
View article: Regulation of the transcriptome, miRNAs, and alternative splicing in a FSGS zebrafish injury model
Regulation of the transcriptome, miRNAs, and alternative splicing in a FSGS zebrafish injury model Open
Background Focal Segmental Glomerulosclerosis (FSGS) is a severe kidney disorder with complex and not yet fully understood pathogenesis. Alternative splicing (AS) – the generation of distinct protein isoforms from the same gene – might pla…
View article: Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing
Comprehensive benchmark of differential transcript usage analysis for bulk and single-cell RNA sequencing Open
RNA sequencing offers unique insights into transcriptome diversity, and a plethora of tools have been developed to analyze alternative splicing. One important task is to detect changes in the relative transcript abundance in differential t…
View article: Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65
Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65 Open
Motivation As most proteins interact with other proteins to perform their respective functions, methods to computationally predict these interactions have been developed. However, flawed evaluation schemes and data leakage in test sets hav…
View article: Single-cell differential expression analysis between conditions within nested settings
Single-cell differential expression analysis between conditions within nested settings Open
Differential expression analysis provides insights into fundamental biological processes and with the advent of single-cell transcriptomics, gene expression can now be studied at the level of individual cells. Many analyses treat cells as …
View article: Refinement strategies for Tangram for reliable single-cell to spatial mapping
Refinement strategies for Tangram for reliable single-cell to spatial mapping Open
Motivation Single-cell RNA sequencing (scRNA-seq) provides comprehensive gene expression data at a single-cell level but lacks spatial context. In contrast, spatial transcriptomics captures both spatial and transcriptional information but …
View article: Functional genomic dissection of MS risk loci reveals convergence of cis and trans gene regulatory mechanisms in microglia
Functional genomic dissection of MS risk loci reveals convergence of cis and trans gene regulatory mechanisms in microglia Open
Summary Neurological diseases (NDs) are a major source of unmet medical need, and translational insights have been hampered by complex underlying pathophysiologies and limitations of experimental models. Noncoding single nucleotide polymor…
View article: From Hype to Health Check: Critical Evaluation of Drug Response Prediction Models with DrEval
From Hype to Health Check: Critical Evaluation of Drug Response Prediction Models with DrEval Open
Motivation Large-scale drug sensitivity screens have enabled training drug response prediction models based on cancer cell line omics profiles to facilitate personalized medicine. While model performances reported in the literature appear …
View article: Extracellular vesicle-associated transcriptomic and proteomic biomarkers show in vitro potential for vandetanib treatment monitoring in anaplastic thyroid cancer
Extracellular vesicle-associated transcriptomic and proteomic biomarkers show in vitro potential for vandetanib treatment monitoring in anaplastic thyroid cancer Open
Background: Anaplastic thyroid cancer (ATC) is an aggressive and rare disease. Rapid metastasis and limited treatments call for additional therapeutic options, including drug repurposing. The early spreading of ATC highlights the importanc…
View article: DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders
DIGGER 2.0: digging into the functional impact of differential splicing on human and mouse disorders Open
Changes in alternative splicing between groups or conditions contribute to protein–protein interaction rewiring, a consequence often neglected in data analysis. The web server and database DIGGER overcomes this limitation by augmenting a p…
View article: Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE
Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE Open
Despite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on isotopic labeling or internal standards in recent decades, systematic biases originating from n…
View article: Integrative Gene and Isoform Co-expression Networks Reveal Regulatory Rewiring in Stress-related Psychiatric Disorders
Integrative Gene and Isoform Co-expression Networks Reveal Regulatory Rewiring in Stress-related Psychiatric Disorders Open
Isoform-specific expression patterns have been implicated in stress-related psychiatric disorders like major depressive disorder (MDD), yet the extent of their involvement and their interrelationships remain unclear. We constructed co-expr…
View article: Unifying DNA methylation-based in silico cell-type deconvolution with <i>deconvMe</i>
Unifying DNA methylation-based in silico cell-type deconvolution with <i>deconvMe</i> Open
Summary Cell-type deconvolution is widely applied to gene expression and DNA methylation data, but access to methods for the latter remains limited. We introduce deconvMe , a new R package that simplifies access to DNA methylation-based de…
View article: Refinement Strategies for Tangram for Reliable Single-Cell to Spatial Mapping
Refinement Strategies for Tangram for Reliable Single-Cell to Spatial Mapping Open
Motivation: Single-cell RNA sequencing (scRNA-seq) provides comprehensive gene expression data at a single-cell level but lacks spatial context. In contrast, spatial transcriptomics captures both spatial and transcriptional information but…
View article: Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE
Systematic Evaluation of Normalization Approaches in Tandem Mass Tag and Label-Free Protein Quantification Data Using PRONE Open
Despite the significant progress in accuracy and reliability in mass spectrometry technology, as well as the development of strategies based on isotopic labeling or internal standards in recent decades, systematic biases originating from n…
View article: Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65
Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65 Open
As most proteins interact with other proteins to perform their respective functions, methods to computationally predict these interactions have been developed. However, flawed evaluation schemes and data leakage in test sets have obscured …
View article: NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data
NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data Open
Background Existing Python libraries and tools lack the ability to efficiently compute statistical test results for large datasets in the presence of missing values. This presents an issue as soon as constraints on runtime and memory avail…
View article: Multi-omic Signatures Relate to the Severity of Pulmonary Outcome in Neonates Traced into Adult Disease
Multi-omic Signatures Relate to the Severity of Pulmonary Outcome in Neonates Traced into Adult Disease Open
Chronic lung disease (CLD) i.e., bronchopulmonary dysplasia (BPD) is the most common long-term complication after preterm birth. This clinically heterogeneous disease is characterized by impaired development of the gas exchange area and th…
View article: Unifying DNA methylation-based <i>in silico</i> cell-type deconvolution with <i>deconvMe</i>
Unifying DNA methylation-based <i>in silico</i> cell-type deconvolution with <i>deconvMe</i> Open
Summary Cell-type deconvolution is widely applied to gene expression and DNA methylation data, but access to methods for the latter remains limited. We introduce deconvMe, a new R package that simplifies access to DNA methylation-based dec…
View article: Emergence of power law distributions in protein-protein interaction networks through study bias
Emergence of power law distributions in protein-protein interaction networks through study bias Open
Degree distributions in protein-protein interaction (PPI) networks are believed to follow a power law (PL). However, technical and study biases affect the experimental procedures for detecting PPIs. For instance, cancer-associated proteins…